Generally, if all of the airplanes in an operator's fleet were bought from the manufacturer and they were received over the period of a couple of years then they will be pretty close in their configuration. But, if it is a large fleet bought over a long period of time then differences will occur. These are generally related to improvements or corrections due to reliability problems. With software driven components, the flight crew will see difference between the earlier and later airplanes. If an operator buys airplanes from the used plane market, then there are likely to be considerable differences between, what seem to be, like airplanes. Manufacturers offer many options in the systems and engines in order to attract as many customers as possible. It's these differences that make a mixed fleet (airplanes built for difference operators) more complicated to operate and maintain.
An airplane that seems to have more than its share of operational and maintenance problems is called a "Hangar Queen". It spends more time than normal in the hangar being repaired. Depending on the operator's philosophy and resources; they may tolerate the situation, they may direct effects in to determining what, in the airplane, is the root cause of these problems and correct them, or they may sell the airplane and pass the problems on to the next guy.